R Under development (unstable) (2026-03-16 r89642 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(HealthMarkers)
> 
> test_check("HealthMarkers")
adipo_is(): computed adipose indices
adipo_is(): preparing inputs
-> adiposity_sds: starting (1 rows, 2 vars)
Completed adiposity_sds_strat
-> adiposity_sds_strat: processing 2 variables for 1 rows
allostatic_load(): computed allostatic load
allostatic_load(): computing (rule >)
-> alm_bmi_index: computing
Completed alm_bmi_index: 1 rows.
-> alm_bmi_index: preparing inputs
Completed alm_bmi_index: 1 rows.
-> bode_index: computing score
Completed bode_index: 1 rows.
-> bode_index: preparing inputs
Completed bode_index: 1 rows.
bone_markers(): completed
bone_markers(): computing bone markers
-> charlson_index: computing
Completed charlson_index: 1 rows.
-> charlson_index: preparing inputs
Completed charlson_index: 1 rows.
-> corrected_calcium: computing result
Completed corrected_calcium: 1 rows.
-> corrected_calcium: preparing inputs
Completed corrected_calcium: 1 rows.
-> corrected_calcium: preparing inputs
-> corrected_calcium: computing result

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/
Saving _problems/test-fasting_is-94.R
[1] "Please use lower # of bins. Current # is 5"
Saving _problems/test-frailty_index-111.R
-> frax_score: computing risk
Completed frax_score: 1 rows.
-> frax_score: preparing inputs
Completed frax_score: 1 rows.
glycemic_markers: validating inputs
-> coercing used columns to numeric
Completed glycemic_markers: 1 rows; NA counts -> SPISE=0, METS_IR=1, prediabetes=1, diabetes=1, HOMA_CP=1, LAR=1, ASI=1, TyG_index=1
glycemic_markers: validating inputs
-> coercing used columns to numeric
-> glycemic_markers: computing markers
-> hormone_markers: starting (1 rows, 17 mapped inputs)
-> iAge: starting
-> iAge: coercing inputs to numeric
Completed iAge: 1 rows; NA(iAge)=0
inflammatory_markers(): computed inflammatory indices
-> kidney_failure_risk: validating inputs
Completed kidney_failure_risk: 1 rows; NA/Inf -> KFRE_2yr=0, KFRE_5yr=0; capped=0; elapsed=0.04s
-> kyn_trp_ratio: computing
Completed kyn_trp_ratio: 1 rows.
-> kyn_trp_ratio: preparing inputs
Completed kyn_trp_ratio: 1 rows.
-> liver_markers: validating inputs
Completed liver_markers: 1 rows; NA/Inf -> FLI=0, NFS=0, APRI=0, FIB4=0, BARD=0, ALBI=0, MELD_XI=0; capped=0; elapsed=0.03s
-> liver_markers: validating inputs
-> liver_markers: computing indices
Completed liver_markers: 1 rows; NA/Inf -> FLI=0, NFS=0, APRI=0, FIB4=0, BARD=0, ALBI=0, MELD_XI=0; capped=0; elapsed=0.05s
-> liver_markers: validating inputs
-> liver_markers: computing indices
-> liver_markers: computing indices
Completed liver_markers: 1 rows; NA/Inf -> FLI=0, NFS=0, APRI=0, FIB4=0, BARD=0, ALBI=0, MELD_XI=0; capped=0; elapsed=0.03s
-> liver_markers: validating inputs
-> liver_markers: computing indices
-> metabolic_risk_features: computing flags
Completed metabolic_risk_features: 1 rows; NA -> dyslipidemia=0, insulin_resistance=0, hyperglycemia=0, hypertension=0; capped=0; elapsed=0.02s
-> metabolic_risk_features: validating inputs
-> metabolic_risk_features: computing flags
Completed metabolic_risk_features: 1 rows; NA -> dyslipidemia=0, insulin_resistance=0, hyperglycemia=0, hypertension=0; capped=0; elapsed=0.05s
-> metss: computing score
Completed metss: 1 rows; NA/Inf=0; key=NHW_M; capped=0; elapsed=0.03s
-> metss: validating inputs
Completed metss: 1 rows; NA/Inf=0; key=NHW_M; capped=0; elapsed=0.03s
-> nfl_marker: computing
Completed nfl_marker: 2 rows.
-> nfl_marker: preparing inputs
Completed nfl_marker: 2 rows.
-> nutrient_markers: computing markers
Completed nutrient_markers: 1 rows; NA/Inf -> FerritinTS=0, AGR=1, Omega3Index=1, Mg_Cr_Ratio=1, GlycatedAlbuminPct=1, UA_Cr_Ratio=1, BUN_Cr_Ratio=1, Ca_x_Phosphate=1, AnionGap=1, Tyr_Phe_Ratio=1; capped=0; denom_zero=0; elapsed=0.01s
-> nutrient_markers: validating inputs
Completed nutrient_markers: 1 rows; NA/Inf -> FerritinTS=0, AGR=1, Omega3Index=1, Mg_Cr_Ratio=1, GlycatedAlbuminPct=1, UA_Cr_Ratio=1, BUN_Cr_Ratio=1, Ca_x_Phosphate=1, AnionGap=1, Tyr_Phe_Ratio=1; capped=0; denom_zero=0; elapsed=0.01s
-> nutrient_markers: validating inputs
-> nutrient_markers: computing markers
-> nutrient_markers: validating inputs
-> nutrient_markers: computing markers
Completed nutrient_markers: 1 rows; NA/Inf -> FerritinTS=0, AGR=1, Omega3Index=1, Mg_Cr_Ratio=1, GlycatedAlbuminPct=1, UA_Cr_Ratio=1, BUN_Cr_Ratio=1, Ca_x_Phosphate=1, AnionGap=1, Tyr_Phe_Ratio=1; capped=0; denom_zero=0; elapsed=0.01s
-> obesity_indices: computing indices
Completed obesity_indices: 2 rows; NA/Inf -> weight_kg=0, height_m=0, BMI=0, BMI_cat=0, WHR=0, waist_to_height_ratio=0, AVI=0, BAI=0, ABSI=0, BRI=0, CI=0, waist_to_BMI_ratio=0, weight_to_height_ratio=0; capped=0; denom_zero=0; elapsed=0.15s
-> obesity_indices: validating inputs
-> obesity_indices: computing indices
-> computing indices
Completed ogtt_is: 1 rows; extremes=0
-> ogtt_is: validating and preparing inputs
Completed ogtt_is: 1 rows; extremes=0
-> pulmo_markers: converting height from cm to m
-> pulmo_markers[GLI]: sex=1; eth=1
-> pulmo_markers: computing markers
Completed pulmo_markers[GLI]: 1 rows; NA/Inf -> fev1_pred=0, fev1_z=0, fev1_pctpred=0, fev1_LLN=0, fvc_pred=0, fvc_z=0, fvc_pctpred=0, fvc_LLN=0, fev1_fvc_ratio=0, fev1_fvc_pred=0, fev1_fvc_z=1, fev1_fvc_pctpred=0, fev1_fvc_LLN=1; elapsed=0.16s
-> pulmo_markers[GLI]: validating inputs
-> pulmo_markers: converting height from cm to m
-> pulmo_markers[GLI]: sex=1; eth=1
Completed pulmo_markers[GLI]: 1 rows; NA/Inf -> fev1_pred=0, fev1_z=0, fev1_pctpred=0, fev1_LLN=0, fvc_pred=0, fvc_z=0, fvc_pctpred=0, fvc_LLN=0, fev1_fvc_ratio=0, fev1_fvc_pred=0, fev1_fvc_z=1, fev1_fvc_pctpred=0, fev1_fvc_LLN=1; elapsed=0.16s
-> renal_markers: computing markers
Completed renal_markers: 1 rows; NA/Inf -> eGFR_cr=0, eGFR_cys=1, eGFR_combined=1, BUN_Cr_ratio=0, FE_Urea=1, NGAL=1, KIM1=1, NAG=1, Beta2Micro=1, IL18=1, L_FABP=1; capped=0; denom_zero=0; elapsed=0.01s
-> renal_markers: validating inputs
Completed renal_markers: 1 rows; NA/Inf -> eGFR_cr=0, eGFR_cys=1, eGFR_combined=1, BUN_Cr_ratio=0, FE_Urea=1, NGAL=1, KIM1=1, NAG=1, Beta2Micro=1, IL18=1, L_FABP=1; capped=0; denom_zero=0; elapsed=0.01s
-> saliva_markers: computing markers
Completed saliva_markers: 1 rows; NA/Inf -> log_cortisol_wake=0, CAR_AUC=0, log_amylase=0, saliva_glucose=0; capped=0; elapsed=0.00s
-> saliva_markers: validating inputs
Completed saliva_markers: 1 rows; NA/Inf -> log_cortisol_wake=0, CAR_AUC=0, log_amylase=0, saliva_glucose=0; capped=0; elapsed=0.01s
-> sarc_f_score: computing
Completed sarc_f_score: 1 rows.
-> sarc_f_score: preparing inputs
Completed sarc_f_score: 1 rows.
Completed spirometry_markers: 1 rows.
-> sweat_markers: computing markers
Completed sweat_markers: 1 rows; NA/Inf -> sweat_chloride=0, Na_K_ratio=0, sweat_lactate=0, sweat_rate=0; capped=0; denom_zero=0; elapsed=0.00s
-> sweat_markers: validating inputs
Completed sweat_markers: 1 rows; NA/Inf -> sweat_chloride=0, Na_K_ratio=0, sweat_lactate=0, sweat_rate=0; capped=0; denom_zero=0; elapsed=0.01s
-> tracer_dxa_is: validating inputs
Completed tracer_dxa_is: 1 rows; NA/Inf -> LIRI_inv=0, Lipo_inv=0, ATIRI_inv=0; capped=0; denom_zero=0; elapsed=0.01s
-> tracer_dxa_is: validating inputs
Completed tracer_dxa_is: 1 rows; NA/Inf -> I_AUC=0, FFA_AUC=0, tracer_palmitate_SI=0, tracer_glycerol_SI=0, LIRI_inv=0, Lipo_inv=0, ATIRI_inv=0; capped=0; denom_zero=0; elapsed=0.01s
-> urine_markers: validating inputs
Completed urine_markers: 1 rows; NA/Inf -> UACR=0, albuminuria_stage=0, microalbuminuria=0, UPCR=1, U_Na_K_ratio=1, NGAL_per_gCr=1, KIM1_per_gCr=1, NAG_per_gCr=1, Beta2Micro_per_gCr=1, A1Micro_per_gCr=1, IL18_per_gCr=1, L_FABP_per_gCr=1; capped=0; denom_zero=0; elapsed=0.01s
-> vitamin_d_status: computing status
Completed vitamin_d_status: 2 rows.
-> vitamin_d_status: preparing inputs
Completed vitamin_d_status: 2 rows.
-> vitamin_markers: computing markers
Completed vitamin_markers: 1 rows; NA/Inf -> VitD_Z=0, B12_Fol_Ratio=0, Ferr_TSat_R=0, Cort_DHEA_R=0, T_E2_Ratio=0, TSH_fT4_R=0, Retinol_Z=0, Toco_Lip_R=0, PIVKA_II=0, VitC=0, Homocysteine=0, MMA=0, Mg_Zn_R=0, Cu_Zn_R=0; capped=0; denom_zero=0; elapsed=0.01s
-> vitamin_markers: validating inputs
Completed vitamin_markers: 1 rows; NA/Inf -> VitD_Z=0, B12_Fol_Ratio=0, Ferr_TSat_R=0, Cort_DHEA_R=0, T_E2_Ratio=0, TSH_fT4_R=0, Retinol_Z=0, Toco_Lip_R=0, PIVKA_II=0, VitC=0, Homocysteine=0, MMA=0, Mg_Zn_R=0, Cu_Zn_R=0; capped=0; denom_zero=0; elapsed=0.02s
-> vitamin_markers: validating inputs
-> vitamin_markers: computing markers
-> vitamin_markers: validating inputs
-> vitamin_markers: computing markers
-> vitamin_markers: validating inputs
-> vitamin_markers: computing markers
[ FAIL 2 | WARN 5 | SKIP 3 | PASS 1319 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• requireNamespace("PooledCohort", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:155:3'
• requireNamespace("QRISK3", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:183:3'
• requireNamespace("RiskScorescvd", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:195:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fasting_is.R:89:3'): verbose = TRUE prints a progress/completion message ──
Error in `expect_message(fasting_is(df, col_map = list(G0 = "G0", I0 = "I0"), verbose = TRUE), "Completed fasting_is:", fixed = TRUE, all = NA)`: `all` must be `TRUE` or `FALSE`, not `NA`.
Backtrace:
    ▆
 1. └─testthat::expect_message(all = NA) at test-fasting_is.R:89:3
 2.   └─testthat:::check_bool(all)
 3.     └─testthat:::stop_input_type(...)
 4.       └─rlang::abort(message, ..., call = call, arg = arg)
── Error ('test-frailty_index.R:107:3'): frailty_index verbose messages ────────
Error in `expect_message(frailty_index(df, cols = c("d1", "d2"), verbose = TRUE), "frailty_index: completed", all = NA)`: `all` must be `TRUE` or `FALSE`, not `NA`.
Backtrace:
    ▆
 1. └─testthat::expect_message(all = NA) at test-frailty_index.R:107:3
 2.   └─testthat:::check_bool(all)
 3.     └─testthat:::stop_input_type(...)
 4.       └─rlang::abort(message, ..., call = call, arg = arg)

[ FAIL 2 | WARN 5 | SKIP 3 | PASS 1319 ]
Error:
! Test failures.
Execution halted